ABSTRACT
Abstract Phylogenetics describes the sequence of speciation events that lead to the forming of a set of current day species. In phylogenetic studies, the most convenient way of visually presenting evolutionary relationships among a group of organisms is through illustrations called phylogenetic trees. Until mid 1950’s phylogenies were often constructed by the subjective criteria based on experts’ opinion about evolution. With the exponential growth of high-throughput whole genome sequencing and data analysis using state of art computational methods and tools, the current era of phylogenetics attempts to determine the rates and patterns of change occurring in DNA and proteins. In this chapter, we will review state of art computational methods and tools available and present an integrative workflow to reconstruct the evolutionary history of regulatory elements for variety of biological applications.
